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Remove aliquot data warning logging #7672

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Merged
XingY merged 2 commits into from
May 19, 2026
+8 −33
Merged

Remove aliquot data warning logging #7672

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0a76538
Only log aliquot data warning once per transaction
XingY May 15, 2026
0e7071e
Drop aliquot field warning logging
XingY May 18, 2026
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30 changes: 5 additions & 25 deletions api/src/org/labkey/api/dataiterator/SimpleTranslator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,6 @@
import org.labkey.api.data.TableSelector;
import org.labkey.api.data.TestSchema;
import org.labkey.api.exp.MvFieldWrapper;
import org.labkey.api.exp.PropertyDescriptor;
import org.labkey.api.exp.PropertyType;
import org.labkey.api.files.FileContentService;
import org.labkey.api.ontology.Unit;
Expand Down Expand Up @@ -486,28 +485,24 @@ protected class DerivationScopedConvertColumn extends SimpleConvertColumn
final int derivationDataColInd;
final int index;
final boolean isDerivation;
final String presentDerivationWarning;
final String presentNonDerivationWarning;

final SimpleConvertColumn _convertCol;

public DerivationScopedConvertColumn(int index, SimpleConvertColumn convertCol, int derivationDataColInd, boolean isDerivation, @Nullable String presentDerivationWarning, @Nullable String presentNonDerivationWarning)
public DerivationScopedConvertColumn(int index, SimpleConvertColumn convertCol, int derivationDataColInd, boolean isDerivation)
{
super(convertCol.fieldName, convertCol.index, convertCol.type, convertCol.defaultUnit);
_convertCol = convertCol;
this.index = index;
this.derivationDataColInd = derivationDataColInd;
this.isDerivation = isDerivation;
this.presentDerivationWarning = presentDerivationWarning;
this.presentNonDerivationWarning = presentNonDerivationWarning;
}

@Override
protected Object convert(Object o)
{
Object thisValue = _convertCol.convert(o);

return getDerivationData(thisValue, derivationDataColInd, isDerivation, presentDerivationWarning, presentNonDerivationWarning);
return getDerivationData(thisValue, derivationDataColInd, isDerivation);

}
}
Expand All @@ -520,48 +515,33 @@ protected class DerivationScopedColumn implements Supplier
final int index;
final boolean isDerivation;

final String presentDerivationWarning;
final String presentNonDerivationWarning;

public DerivationScopedColumn(int index, int derivationDataColInd, boolean isDerivation, @Nullable String presentDerivationWarning, @Nullable String presentNonDerivationWarning)
public DerivationScopedColumn(int index, int derivationDataColInd, boolean isDerivation)
{
this.index = index;
this.derivationDataColInd = derivationDataColInd;
this.isDerivation = isDerivation;
this.presentDerivationWarning = presentDerivationWarning;
this.presentNonDerivationWarning = presentNonDerivationWarning;
}

@Override
public Object get()
{
Object thisValue = _data.get(index);
return getDerivationData(thisValue, derivationDataColInd, isDerivation, presentDerivationWarning, presentNonDerivationWarning);
return getDerivationData(thisValue, derivationDataColInd, isDerivation);
}
}

/**
* @param thisValue the original field value
* @param derivationDataColInd the col index for the field used to determine if a record is child or parent
* @param isDerivationField if this field is a child only field
* @param presentDerivationWarning the warning msg to log if a child field is present for a parent record
* @param presentNonDerivationWarning the warning msg to log if a parent field is present for a child record
*/
private Object getDerivationData(Object thisValue, int derivationDataColInd, boolean isDerivationField, @Nullable String presentDerivationWarning, @Nullable String presentNonDerivationWarning)
private Object getDerivationData(Object thisValue, int derivationDataColInd, boolean isDerivationField)
{
Object derivationData = derivationDataColInd < 0 ? null : _data.get(derivationDataColInd);
if ((isDerivationField && derivationData != null)
|| (!isDerivationField && derivationData == null))
return thisValue;

if (thisValue != null)
{
if (isDerivationField && presentDerivationWarning != null)
LOG.warn(presentDerivationWarning);
else if (!isDerivationField && presentNonDerivationWarning != null)
LOG.warn(presentNonDerivationWarning);
}

return null;
}

Expand Down
11 changes: 3 additions & 8 deletions experiment/src/org/labkey/experiment/api/SampleTypeUpdateServiceDI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1753,9 +1753,6 @@ private boolean rowExists(String name)

static class _SamplesCoerceDataIterator extends SimpleTranslator
{
private static final String INVALID_ALIQUOT_PROPERTY = "An aliquot-specific property [%1$s] value has been ignored for a non-aliquot sample.";
private static final String INVALID_NON_ALIQUOT_PROPERTY = "A sample property [%1$s] value has been ignored for an aliquot.";

private final ExpSampleTypeImpl _sampleType;
private final Unit _sampleTypeBaseUnit;

Expand Down Expand Up @@ -1810,14 +1807,12 @@ else if (amountImportAliasSet.contains(from.getName()))
String name = to.getName();
boolean isScopedField = scopedFields.containsKey(name);

String ignoredAliquotPropValue = String.format(INVALID_ALIQUOT_PROPERTY, name);
String ignoredMetaPropValue = String.format(INVALID_NON_ALIQUOT_PROPERTY, name);
if (to.getPropertyType() == PropertyType.ATTACHMENT || to.getPropertyType() == PropertyType.FILE_LINK)
{
if (isScopedField)
{
ColumnInfo clone = new BaseColumnInfo(to);
addColumn(clone, new DerivationScopedColumn(i, aliquotedFromDataColInd, scopedFields.get(name), ignoredAliquotPropValue, ignoredMetaPropValue));
addColumn(clone, new DerivationScopedColumn(i, aliquotedFromDataColInd, scopedFields.get(name)));
}
else
addColumn(to, i);
Expand All @@ -1829,7 +1824,7 @@ else if (to.isMultiValued() || to.getFk() instanceof MultiValuedForeignKey)
{
var col = new BaseColumnInfo(getInput().getColumnInfo(i));
col.setName(name);
addColumn(col, new DerivationScopedColumn(i, aliquotedFromDataColInd, scopedFields.get(name), ignoredAliquotPropValue, ignoredMetaPropValue));
addColumn(col, new DerivationScopedColumn(i, aliquotedFromDataColInd, scopedFields.get(name)));
}
else
addColumn(to.getName(), i);
Expand Down Expand Up @@ -1900,7 +1895,7 @@ private void _addConvertColumn(String name, int fromIndex, JdbcType toType, @Nul
private void _addConvertColumn(ColumnInfo col, int fromIndex, int derivationDataColInd, boolean isAliquotField)
{
SimpleConvertColumn c = createConvertColumn(col, fromIndex, RemapMissingBehavior.Error);
c = new DerivationScopedConvertColumn(fromIndex, c, derivationDataColInd, isAliquotField, String.format(INVALID_ALIQUOT_PROPERTY, col.getName()), String.format(INVALID_NON_ALIQUOT_PROPERTY, col.getName()));
c = new DerivationScopedConvertColumn(fromIndex, c, derivationDataColInd, isAliquotField);

addColumn(col, c);
}
Expand Down